A Shadowing Problem in the Detection of Overlapping Communities: Lifting the Resolution Limit through a Cascading Procedure

Community detection is the process of assigning nodes and links in significant communities (e.g. clusters, function modules) and its development has led to a better understanding of complex networks. When applied to sizable networks, we argue that most detection algorithms correctly identify prominent communities, but fail to do so across multiple scales. As a result, a significant fraction of the network is left uncharted. We show that this problem stems from larger or denser communities overshadowing smaller or sparser ones, and that this effect accounts for most of the undetected communities and unassigned links. We propose a generic cascading approach to community detection that circumvents the problem. Using real and artificial network datasets with three widely used community detection algorithms, we show how a simple cascading procedure allows for the detection of the missing communities. This work highlights a new detection limit of community structure, and we hope that our approach can inspire better community detection algorithms.     

Bringing European river quality into line: an exercise to intercalibrate macro-invertebrate classification methods

The Water Framework Directive (WFD) requires intercalibration to be performed to ensure that ecological status, as defined by the boundary values of national biological assessment systems, is consistent with the definitions outlined in the WFD and comparable between Member States (MS). This article describes an intercalibration of 17 national river macro-invertebrate assessment methods from the Central and Baltic regions of Europe. We explore the hypothesis that intercalibration should be successful if ratios of the observed biota to that expected in reference condition are used to compare assessments of different national assessment systems. National boundaries expressed as ecological quality ratios (EQRs) were converted to values of a common multi-metric for the purpose of comparison. Twelve MS for the High/Good boundary and nine MS for the Good/Moderate boundary (and four MS who subsequently harmonised their boundaries) were within ±0.05 EQR units of the intercalibration boundaries and were deemed to be of comparable ecological standard. The use of a reference-based approach was deemed to be successful given that all the critical pre-requisites for intercalibration were satisfied. The boundaries derived from this intercalibration represent the first common interpretation of the ecological status of rivers based on macro-invertebrate assessment methods across Europe.     

Combining modelling and mutagenesis studies of synaptic vesicle protein 2A to identify a series of residues involved in racetam binding

LEV (levetiracetam), an antiepileptic drug which possesses a unique profile in animal models of seizure and epilepsy, has as its unique binding site in brain, SV2A (synaptic vesicle protein 2A). Previous studies have used a chimaeric and site-specific mutagenesis approach to identify three residues in the putative tenth transmembrane helix of SV2A that, when mutated, alter binding of LEV and related racetam derivatives to SV2A. In the present paper, we report a combined modelling and mutagenesis study that successfully identifies another 11 residues in SV2A that appear to be involved in ligand binding. Sequence analysis and modelling of SV2A suggested residues equivalent to critical functional residues of other MFS (major facilitator superfamily) transporters. Alanine scanning of these and other SV2A residues resulted in the identification of residues affecting racetam binding, including Ile273 which differentiated between racetam analogues, when mutated to alanine. Integrating mutagenesis results with docking analysis led to the construction of a mutant in which six SV2A residues were replaced with corresponding SV2B residues. This mutant showed racetam ligand-binding affinity intermediate to the affinities observed for SV2A and SV2B.     

Testing local and global stressor impacts on a coastal foundation species using an ecologically realistic framework

Despite the abundance of literature on organismal responses to multiple environmental stressors, most studies have not matched the timing of experimental manipulations with the temporal pattern of stressors in nature. We test the interactive effects of diel‐cycling hypoxia with both warming and decreased salinities using ecologically realistic exposures. Surprisingly, we found no evidence of negative synergistic effects on Olympia oyster growth; rather, we found only additive and opposing effects of hypoxia (detrimental) and warming (beneficial). We suspect that diel‐cycling provided a temporal refuge that allowed physiological compensation. We also tested for latent effects of warming and hypoxia to low‐salinity tolerance using a seasonal delay between stressor events. However, we did not find a latent effect, rather a threshold survival response to low salinity that was independent of early life‐history exposure to warming or hypoxia. The absence of synergism is likely the result of stressor treatments that mirror the natural timing of environmental stressors. We provide environmental context for laboratory experimental data by examining field time series environmental data from four North American west coast estuaries and find heterogeneous environmental signals that characterize each estuary, suggesting that the potential stressor exposure to oysters will drastically differ over moderate spatial scales. This heterogeneity implies that efforts to conserve and restore oysters will require an adaptive approach that incorporates knowledge of local conditions. We conclude that studies of multiple environmental stressors can be greatly improved by integrating ecologically realistic exposure and timing of stressors found in nature with organismal life‐history traits.     

Deoxynucleoside overproduction in deoxyadenosine-resistant, adenosine deaminase-deficient human histiocytic lymphoma cells

Deoxyadenosine toxicity toward lymphocytes may produce immune dysfunction in patients with adenosine deaminase (adenosine aminohydrolase, EC 3.5.4.4) deficiency. The relationship between endogenous deoxynucleoside synthesis in adenosine deaminase-deficient cells and sensitivity to adenosine and deoxyadenosine toxicity is unclear. The human histiocytic lymphoma cell line (DHL-9) naturally lacks adenosine deaminase, and has minimal levels of thymidine kinase. Dividing DHL-9 cells excrete deoxyadenosine and thymidine into the extracellular space. The present experiments have analyzed nucleoside synthesis and excretion in a mutagenized clone of DHL-9 cells, selected for increased resistance to deoxyadenosine toxicity. The deoxyadenosine-resistant cells excreted both deoxyadenosine and thymidine at a 6-7-fold higher rate than wild-type lymphoma cells. The deoxyadenosine overproduction was accompanied by a reduced ability to form dATP from exogenous deoxyadenosine, and a 2.5-fold increase in ribonucleotide reductase activity. The pace of adenosine excretion, the growth rate, and the levels of multiple other enzymes involved in deoxyadenosine and adenosine metabolism were equivalent in the two cell types. These results suggest that the excretion of deoxyadenosine and thymidine, but not adenosine, is exquisitely sensitive to alterations in the rate of endogenous deoxynucleotide synthesis. Apparently, small changes in deoxynucleotide synthesis can significantly influence cellular sensitivity to deoxyadenosine toxicity.     

Inhibition of DNA repair by deoxyadenosine in resting human lymphocytes

Profound lymphopenia is characteristic of immunodeficient children who lack adenosine deaminase (ADA). When ADA is inactive, deoxyadenosine (dAdo) is phosphorylated by immature T lymphoblasts and inhibits cell division. However, dAdo also causes the slow accumulation of DNA strand breaks in nondividing, mature human peripheral blood lymphocytes. To explore the basis for this phenomenon, we have assessed the effects of dAdo and other deoxynucleosides on the repair of gamma-radiation induced DNA strand breaks in resting normal lymphocyte cultures. As measured by a sensitive DNA unwinding assay, most DNA strand breaks were rejoined within 2 hr after exposure of lymphocytes to 500 rad. In medium supplemented with deoxycoformycin, a tight binding ADA inhibitor, dAdo retarded DNA rejoining in a dose and time dependent manner. The inhibition required dAdo phosphorylation. Over an 8-hr period, 10 microM dAdo gradually rendered peripheral blood lymphocytes incompetent for DNA repair. Among several other compounds tested, 2-chlorodeoxyadenosine, an ADA resistant dAdo congener with anti-leukemic and immunosuppressive activity, was the most powerful inhibitor of DNA repair, exerting significant activity at concentrations as low as 100 nM. Both dAdo and 2-chlorodeoxyadenosine blocked unscheduled DNA synthesis in irradiated resting lymphocytes, as measured by [3H]thymidine uptake. On the basis of this and other data, we suggest that quiescent peripheral blood lymphocytes break and rejoin DNA at a slow and balanced rate. The accumulation of dATP progressively retards the DNA repair process and thereby fosters the time-dependent accretion of DNA strand breaks. By inhibiting DNA repair, dAdo, 2-chlorodeoxyadenosine and related compounds may substantially potentiate the toxicity of DNA damaging agents to normal and malignant lymphocytes.     

Post genome-wide association studies of novel genes associated with type 2 diabetes show gene-gene interaction and high predictive value

Background

Recently, several Genome Wide Association (GWA) studies in populations of European descent have identified and validated novel single nucleotide polymorphisms (SNPs), highly associated with type 2 diabetes (T2D). Our aims were to validate these markers in other European and non-European populations, then to assess their combined effect in a large French study comparing T2D and normal glucose tolerant (NGT) individuals.

Methodology/Principal Findings

In the same French population analyzed in our previous GWA study (3,295 T2D and 3,595 NGT), strong associations with T2D were found for CDKAL1 (OR_rs7756992 = 1.30[1.19–1.42], P = 2.3×10⁻⁹), CDKN2A/2B (OR_rs10811661 = 0.74[0.66–0.82], P = 3.5×10⁻⁸) and more modestly for IGFBP2 (OR_rs1470579 = 1.17[1.07–1.27], P = 0.0003) SNPs. These results were replicated in both Israeli Ashkenazi (577 T2D and 552 NGT) and Austrian (504 T2D and 753 NGT) populations (except for CDKAL1) but not in the Moroccan population (521 T2D and 423 NGT). In the overall group of French subjects (4,232 T2D and 4,595 NGT), IGFBP2 and CXCR4 synergistically interacted with (LOC38776, SLC30A8, HHEX) and (NGN3, CDKN2A/2B), respectively, encoding for proteins presumably regulating pancreatic endocrine cell development and function. The T2D risk increased strongly when risk alleles, including the previously discovered T2D-associated TCF7L2 rs7903146 SNP, were combined (8.68-fold for the 14% of French individuals carrying 18 to 30 risk alleles with an allelic OR of 1.24). With an area under the ROC curve of 0.86, only 15 novel loci were necessary to discriminate French individuals susceptible to develop T2D.

Conclusions/Significance

In addition to TCF7L2, SLC30A8 and HHEX, initially identified by the French GWA scan, CDKAL1, IGFBP2 and CDKN2A/2B strongly associate with T2D in French individuals, and mostly in populations of Central European descent but not in Moroccan subjects. Genes expressed in the pancreas interact together and their combined effect dramatically increases the risk for T2D, opening avenues for the development of genetic prediction tests.     

Fungal infections of a colonial marine invertebrate: Diversity and morphological consequences

Summary Colonies of the bryozoan speciesHippodiplosia insculpta collected from Grandmother’s Cove (American Camp, San Juan Island, Washington, USA) were analyzed in view of pathologic growth patterns. The species produced giant buds that were filled with extracellular polymeric substances and a dense microbial biofilm consisting of bacteria and fungal hyphae. Fungi were isolated from the colonies and were identified asPenicillium expansum, Peniillium brevicompactum, Sclerotinia sclerotiorum, Acremonium breve, andCladosporium sphaerospermum. The results of this study indicate that the formation of giant buds in the bryozoan is a defense mechanism against fungal infection.     

Impacts and interactions of multiple human perturbations in a California salt marsh

Multiple disturbances to ecosystems can influence community structure by modifying resistance to and recovery from invasion by non-native species. Predicting how invasibility responds to multiple anthropogenic impacts is particularly challenging due to the variety of potential stressors and complex responses. Using manipulative field experiments, we examined the relative impact of perturbations that primarily change abiotic or biotic factors to promote invasion in coastal salt marsh plant communities. Specifically we test the hypotheses that nitrogen enrichment and human trampling facilitate invasion of upland weeds into salt marsh, and that the ability of salt marsh communities to resist and/or recover from invasion is modified by hydrological conditions. Nitrogen enrichment affected invasion of non-native upland plants at only one of six sites, and increased aboveground native marsh biomass at only two sites. Percent cover of native marsh plants declined with trampling at all sites, but recovered earlier at tidally flushed sites than at tidally restricted sites. Synergistic interactions between trampling and restricting tidal flow resulted in significantly higher cover of non-native upland plants in trampled plots at tidally restricted sites. Percent cover of non-native plants recovered to pre-trampling levels in fully tidal sites, but remained higher in tidally restricted sites after 22 months. Thus, perturbations that reduce biotic resistance interact with perturbations that alter abiotic conditions to promote invasion. This suggests that to effectively conserve or restore native biodiversity in altered systems, one must consider impacts of multiple human disturbances, and the interactions between them. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.